Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6047 |
| PDBID: | 8DUL |
| Chains: | HL_A |
| Organism: | Western equine encephalitis virus, Macaca fascicularis |
| Method: | EM |
| Resolution (Å): | 4.17 |
| Reference: | 10.1016/j.cell.2023.05.019 |
| Antibody | |
| Antibody: | SKT05 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Western equine encephalitis virus-like particle (VLP) spike glycoprotein E1 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8DUL_H|Chain G[auth H]|Antibody Fab SKT05 heavy chain|Macaca fascicularis (9541) EVQLVESGAGLVQPGGSLRLSCAASGFTFSDSWMSWVRQSPGKGLEWVGRIKGKPDGETAAYAASVKGRFSISRDDSKNTLYLQMNSLKTEDTAVYYCTRDDRTSCRRGVCYAAFHSWGQGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGLEVLFQ |
Light Chain: L
Mutation: NULL
| >8DUL_L|Chain H[auth L]|Antibody Fab SKT05 light chain|Macaca fascicularis (9541) DIQMTQSPSSLSASAGDRVTLTCRASQAISFYLAWYQQKPGKAPKRLIYDASELQGGVPSRFSGSGSGTDFTLSINSLQPEDSATYFCLQYDSPPFTFGPGTKVEIKRTVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLTLSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >8DUL_A|Chain B[auth A], D[auth F], F[auth J]|Spike glycoprotein E1|Western equine encephalitis virus (11039) RPTNAETFGETLNHLWFNNQPFLWAQLCIPLAALVILFRCFSCCMPFLLVAGVCLGKVDAFEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCRFHTVIPSPQVKCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAVALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIRKGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGYEMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVSCTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSSPQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSLIVVGLIVLV |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| H: ASP31 SER32 ARG94 ASP95 ASP96 ARG97 THR98 SER99 HIS101 L: PHE31 TYR49 ASP50 SER52 GLU53 LEU54 GLY56 GLY57 VAL58 SER60 A: CYS63 SER65 LEU66 GLU67 CYS68 LYS69 ALA70 SER71 ASP75 TYR76 THR77 CYS78 ARG79 VAL80 PHE81 GLY82 GLY83 SER98 GLU99 ASN100 THR101 ALA215 ARG216 ASP218 ILE219 LYS223 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
